At the time of the Cylon attack, Heracles was under the command of Commander Tasha Dannel. The Heracles and her battlegroup were conducting a standard deterrence patrol near Virgon when word of the attack began to filter out to the fleet. Immediately departing their patrol route, the Heracles and her group proceeded to the nearest emergency fleet rally point listed in their Emergency War Orders while they awaited further orders from Picon Fleet Headquarters. Following the destruction of Fleet HQ, the order went out over the wireless for all remaining units to rendezvous with Admiral Nagala aboard the Battlestar Atlantia for a counterattack.

After linking up with the Atlantia and four other surviving Battlestar Groups, Heracles' group was assigned by Admiral Nagala to act as a reserve force while the other ships attempted to counter-attack a Cylon task force near Virgon. With the nature of the computer failures that were plaguing Colonial equipment still an unkown factor, Commander Dannel and her officers and crew were helpless as they watched Admiral Nagala's counter-attack falter and fail, the entire contingent of five Battlestar Groups being wiped out in a matter of minutes.

Ordering her group into a immediate retreat, Commander Dannel initially spared her group from suffering the same fate as they proceeded away from the immediate combat zone in order to attempt a link up with any other surviving units. Regrettably, the Cylons found the Heracles first. While loitering near one of their assigned rally points, Heracles and her group came under attack by a Hunter-Killer group of Raiders that managed to exploit the computer vulnerability and shut down all systems aboard the Colonial ships. Athlought her heavy combat assets were now neutralized, Dannel had fortuitously gambled by placing a Reserve unit of older Mark Six Vipers as her alert squadron. Nevertheless, even as these planes sortied for a counter-attack, the Heracles and her group came under punnishing assault, two of her escorts being destroyed outright while a section of Heavy Raiders landed on the HeraclesPort flight pod and unloaded a boarding force of Centurions. Soon after the boarding action began, a massive detonation all but destroyed the Port pod. Although the Mark Six Vipers aloft eventually managed to destroy all the attacking Raiders and Heavy Raiders, the damage had already been done; all four vessels in Heracles' group were either destroyed or rendered unserviceable. The Heracles herself, in addition to the loss of her Port pod, also suffered significant damage to her aft engineering spaces ensuring the vessel would never again be able to operate under her own power. In addition, a section of the Cylon Centurion boarding force managed to penetrate all the way up the Heracles CIC and systematically assasinated the entire command staff, including Commander Dannel.

For the Heracles and her group, the war was all but over. For the survivors, both aboard the few Vipers aloft, as well as those crewmembers huddled within the powerless hull, their fates seemed all but sealed; a cold, suffocating death in the depths of space.

Soon after the crippling attack, however, the Warstar Galactica arrived and collected up the surviving crew and supplies from the battered force. In a final gesture to honor the loss of the Heracles and her group, the commander of the Warstar Galactica, Commander Sean Kelso, retrieved the Heracles' commissioning plaque. It currently rests along with other reminders and mementos from the Fall of the Colonies aboard the former Battlestar Pacifica near the Wall of Rememberance.